My son had reflux as well. I don't think crying makes the reflux worse. Sucking actually helps sooth the burning of reflux, so that may be why your lo wants to eat at naptime. Have you tried a pacifier as part of the winddown time before bed instead of nursing. How often is your lo eating? I would be cautious about saying that there is no accidental parenting with reflux babies. True, getting rid of the pain is very important, but you also don't want to set yourself up as a prop once the pain is under control. I am glad the meds seem to be helping. So, now that you are helping his pain, I would suggest getting on a routine.
It is okay to use w2s and pu/pd and shh/pat as long as you know your lo isn't in pain and just needing help getting to sleep. When you said you tried w2s and he cried for over an hour, how did you do the w2s? Did you fully wake him or did you just get him to stir? Why are you doing w2s in the night and what time? Can you give an idea of your typical day/ routine? Sorry so many questions, just trying to get the whole picture.